[med-svn] [SCM] picard-tools branch, master, updated. upstream/1.41-29-g3a1681d

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 3a1681dc47839538cb988eb664a5c330dc48468b
Author: Shaun Jackman <sjackman at debian.org>
Date:   Tue Mar 22 10:59:07 2011 -0700

    * New upstream release. Closes: #619201.
    * Add five commands to bin/picard-tools and picard-tools.1.

diff --git a/debian/bin/picard-tools b/debian/bin/picard-tools
index 0840841..f529f7d 100755
--- a/debian/bin/picard-tools
+++ b/debian/bin/picard-tools
@@ -15,6 +15,8 @@ else
 fi
 
 case $command in
+	AddOrReplaceReadGroups)         main=net.sf.picard.sam.AddOrReplaceReadGroups;;
+	BamIndexStats)                  main=net.sf.picard.sam.BamIndexStats;;
 	BamToBfq)                       main=net.sf.picard.fastq.BamToBfq;;
 	BuildBamIndex)                  main=net.sf.picard.util.BuildBamIndex;;
 	CalculateHsMetrics)             main=net.sf.picard.analysis.directed.CalculateHsMetrics;;
@@ -22,9 +24,11 @@ case $command in
 	CollectAlignmentSummaryMetrics) main=net.sf.picard.analysis.CollectAlignmentSummaryMetrics;;
 	CollectGcBiasMetrics)           main=net.sf.picard.analysis.CollectGcBiasMetrics;;
 	CollectInsertSizeMetrics)       main=net.sf.picard.analysis.CollectInsertSizeMetrics;;
+	CollectMultipleMetrics)         main=net.sf.picard.analysis.CollectMultipleMetrics;;
 	CompareSAMs)                    main=net.sf.picard.sam.CompareSAMs;;
 	CreateSequenceDictionary)       main=net.sf.picard.sam.CreateSequenceDictionary;;
 	EstimateLibraryComplexity)      main=net.sf.picard.sam.EstimateLibraryComplexity;;
+	ExtractSequences)               main=net.sf.picard.reference.ExtractSequences;;
 	FastqToSam)                     main=net.sf.picard.sam.FastqToSam;;
 	FixMateInformation)             main=net.sf.picard.sam.FixMateInformation;;
 	MarkDuplicates)                 main=net.sf.picard.sam.MarkDuplicates;;
@@ -33,6 +37,7 @@ case $command in
 	MergeSamFiles)                  main=net.sf.picard.sam.MergeSamFiles;;
 	NormalizeFasta)                 main=net.sf.picard.reference.NormalizeFasta;;
 	QualityScoreDistribution)       main=net.sf.picard.analysis.QualityScoreDistribution;;
+	ReorderSam)                     main=net.sf.picard.sam.ReorderSam;;
 	ReplaceSamHeader)               main=net.sf.picard.sam.ReplaceSamHeader;;
 	RevertSam)                      main=net.sf.picard.sam.RevertSam;;
 	SamFormatConverter)             main=net.sf.picard.sam.SamFormatConverter;;
diff --git a/debian/changelog b/debian/changelog
index c088c32..44b7f97 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+picard-tools (1.41-1) unstable; urgency=low
+
+  * New upstream release. Closes: #619201.
+  * Add five commands to bin/picard-tools and picard-tools.1.
+
+ -- Shaun Jackman <sjackman at debian.org>  Tue, 22 Mar 2011 10:52:23 -0700
+
 picard-tools (1.27-1) unstable; urgency=low
 
   * New upstream release.
diff --git a/debian/picard-tools.1 b/debian/picard-tools.1
index a48bbfb..fd7672e 100644
--- a/debian/picard-tools.1
+++ b/debian/picard-tools.1
@@ -8,6 +8,8 @@ SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments.
 
 Picard Tools includes these utilities to manipulate SAM and BAM files:
+ AddOrReplaceReadGroups
+ BamIndexStats
  BamToBfq
  BuildBamIndex
  CalculateHsMetrics
@@ -15,9 +17,11 @@ Picard Tools includes these utilities to manipulate SAM and BAM files:
  CollectAlignmentSummaryMetrics
  CollectGcBiasMetrics
  CollectInsertSizeMetrics
+ CollectMultipleMetrics
  CompareSAMs
  CreateSequenceDictionary
  EstimateLibraryComplexity
+ ExtractSequences
  FastqToSam
  FixMateInformation
  MarkDuplicates
@@ -26,6 +30,7 @@ Picard Tools includes these utilities to manipulate SAM and BAM files:
  MergeSamFiles
  NormalizeFasta
  QualityScoreDistribution
+ ReorderSam
  ReplaceSamHeader
  RevertSam
  SamFormatConverter

-- 
manipulate SAM and BAM files